Do the board investigations whenever they become available because they each give a trophy (you get a warning before going to bed if one is available).Killing enemies (armed humans and monsters) is fine.
Each day has a main quest, after finishing it you use the Portal Generator to return to your base, here you can spend the evening to build new items and learn new skills from teammates, then go to bed, then wake up the next day and play another main quest. The game is divided into 25 days, basically the chapters. All teammates are met automatically in the story and you get a dialogue to recruit them or to send them away. Then you revive at the same day/quest when you died, you don’t need to replay the story. When you die you go to the “afterlife dimension” and spend Chernobylite to change any story decisions from earlier. You just need to watch out that you recruit all 4 optional teammates, but even if you miss this you can change your story choices retroactively whenever you die, so nothing is missable. Welcome to the Chernobylite Trophy Guide (Achievement Guide)! This is an incredibly easy and straightforward platinum because all trophies come automatically from the story.